Agreed. The least effective developers I’ve had the displeasure of working with never understand how their code executes end-to-end. And the best ones have a deep knowledge of it.

This is no fluke! If you don’t know how a classloader works with the Java classpath, how to set various JVM flags for operating the JVM, etc., then I’d argue that you’re an amateur, and I wouldn’t trust you to write correct code in a production setting. It’s critical knowledge to know how your code runs, and if you don’t know that, then stay away from production systems. If the goal of these courses is to teach students enough about Java to use it in a professional setting, then knowing how classfiles are produced, bundled, distributed, loaded, and executed by a JVM is critical knowledge.

More succinctly, if you don’t know how your code makes it to a production server and gets executed, you’re not ready to work on it.

(And if the goal isn't to teach students how to use Java in a professional setting, then why are they learning it at all? Use a teaching language so students can focus on the concepts instead of Java's idiosyncracies.)